

<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
  <meta charset="utf-8">
  
  <meta name="viewport" content="width=device-width, initial-scale=1.0">
  
  <title>compute atom/molecule command &mdash; LIGGGHTS v3.X documentation</title>
  

  
  
  
  

  

  
  
    

  

  
  
    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
  

  

  
    <link rel="top" title="LIGGGHTS v3.X documentation" href="index.html"/> 

  
  <script src="_static/js/modernizr.min.js"></script>

</head>

<body class="wy-body-for-nav" role="document">

   
  <div class="wy-grid-for-nav">

    
    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
      <div class="wy-side-scroll">
        <div class="wy-side-nav-search">
          

          
            <a href="Manual.html" class="icon icon-home"> LIGGGHTS
          

          
          </a>

          
            
            
              <div class="version">
                v3.X
              </div>
            
          

          
<div role="search">
  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
    <input type="text" name="q" placeholder="Search docs" />
    <input type="hidden" name="check_keywords" value="yes" />
    <input type="hidden" name="area" value="default" />
  </form>
</div>

          
        </div>

        <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
          
            
            
              
            
            
              <ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_input_script.html">3. Input Script</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">4. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_gran_models.html">5. Contact models</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_mesh_modules.html">6. Mesh modules</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">7. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">8. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">9. Modifying &amp; extending LIGGGHTS(R)-PUBLIC</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">10. Python interface to LIGGGHTS(R)-PUBLIC</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">11. Errors</a></li>
</ul>

            
          
        </div>
      </div>
    </nav>

    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">

      
      <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
        
          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
          <a href="Manual.html">LIGGGHTS</a>
        
      </nav>


      
      <div class="wy-nav-content">
        <div class="rst-content">
          















<div role="navigation" aria-label="breadcrumbs navigation">

  <ul class="wy-breadcrumbs">
    
      <li><a href="Manual.html">Docs</a> &raquo;</li>
        
      <li>compute atom/molecule command</li>
    
    
      <li class="wy-breadcrumbs-aside">
        
            
            <a href="_sources/compute_atom_molecule.txt" rel="nofollow"> View page source</a>
          
          <a href="http://www.cfdem.com"> Website</a>
          
            <a href="Section_commands.html#comm" rel="nofollow"> Commands</a>
            
          
        
      </li>
    
  </ul>

  
  <hr/>
  
</div>
          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
           <div itemprop="articleBody">
            
  <div class="section" id="compute-atom-molecule-command">
<span id="index-0"></span><h1>compute atom/molecule command<a class="headerlink" href="#compute-atom-molecule-command" title="Permalink to this headline">¶</a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID atom/molecule general_keywords general_values input1 input2 ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>atom/molecule = style name of this compute command</li>
<li>general_keywords general_values are documented in <a class="reference external" href="compute.html&quot;">compute</a></li>
<li>one or more inputs can be listed</li>
<li>input = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
</ul>
<div class="highlight-python"><div class="highlight"><pre>c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
v_name = per-atom vector calculated by an atom-style variable with name
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all atom/molecule c_ke c_pe
compute 1 top atom/molecule v_myFormula c_stress**3**
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Define a calculation that sums per-atom values on a per-molecule
basis, one per listed input.  The inputs can <a class="reference internal" href="compute.html"><em>computes</em></a>,
<a class="reference internal" href="fix.html"><em>fixes</em></a>, or <a class="reference internal" href="variable.html"><em>variables</em></a> that generate per-atom
quantities.  Note that attributes stored by atoms, such as mass or
force, can also be summed on a per-molecule basis, by accessing these
quantities via the <a class="reference internal" href="compute_property_atom.html"><em>compute property/atom</em></a>
command.</p>
<p>Each listed input is operated on independently.  Only atoms within the
specified group contribute to the per-molecule sum.  Note that compute
or fix inputs define their own group which may affect the quantities
they return.  For example, if a compute is used as an input which
generates a per-atom vector, it will generate values of 0.0 for atoms
that are not in the group specified for that compute.</p>
<p>The ordering of per-molecule quantities produced by this compute is
consistent with the ordering produced by other compute commands that
generate per-molecule datums.  Conceptually, them molecule IDs will be
in ascending order for any molecule with one or more of its atoms in
the specified group.</p>
<p>If an input begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
previously defined in the input script and which generates per-atom
quantities.  See the individual <a class="reference internal" href="compute.html"><em>compute</em></a> doc page for
details.  If no bracketed integer is appended, the vector calculated
by the compute is used.  If a bracketed integer is appended, the Ith
column of the array calculated by the compute is used.  Users can also
write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><em>add them to LIGGGHTS(R)-PUBLIC</em></a>.</p>
<p>If an input begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
previously defined in the input script and which generates per-atom
quantities.  See the individual <a class="reference internal" href="fix.html"><em>fix</em></a> doc page for details.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with when compute atom/molecule references
the values, else an error results.  If no bracketed integer is
appended, the vector calculated by the fix is used.  If a bracketed
integer is appended, the Ith column of the array calculated by the fix
is used.  Users can also write code for their own fix style and <a class="reference internal" href="Section_modify.html"><em>add them to LIGGGHTS(R)-PUBLIC</em></a>.</p>
<p>If an input begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has
been previously defined in the input script.  It must be an
<a class="reference internal" href="variable.html"><em>atom-style variable</em></a>.  Atom-style variables can
reference thermodynamic keywords and various per-atom attributes, or
invoke other computes, fixes, or variables when they are evaluated, so
this is a very general means of generating per-atom quantities to sum
on a per-molecule basis.</p>
<hr class="docutils" />
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector or global array depending on
the number of input values.  The length of the vector or number of
rows in the array is the number of molecules.  If a single input is
specified, a global vector is produced.  If two or more inputs are
specified, a global array is produced where the number of columns =
the number of inputs.  The vector or array can be accessed by any
command that uses global values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-8"><span>this section</span></a> for an overview of LIGGGHTS(R)-PUBLIC output
options.</p>
<p>All the vector or array values calculated by this compute are
&#8220;extensive&#8221;.</p>
<p>The vector or array values will be in whatever <a class="reference internal" href="units.html"><em>units</em></a> the
input quantities are in.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="compute.html"><em>compute</em></a>, <a class="reference internal" href="fix.html"><em>fix</em></a>, <a class="reference internal" href="variable.html"><em>variable</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>


           </div>
           <div class="articleComments">
            
           </div>
          </div>
          <footer>
  

  <hr/>

  <div role="contentinfo">
    <p>
        &copy; Copyright 2016, DCS Computing GmbH, JKU Linz and Sandia Corporation.

    </p>
  </div>
  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 

</footer>

        </div>
      </div>

    </section>

  </div>
  


  

    <script type="text/javascript">
        var DOCUMENTATION_OPTIONS = {
            URL_ROOT:'./',
            VERSION:'v3.X',
            LANGUAGE:'None',
            COLLAPSE_INDEX:false,
            FILE_SUFFIX:'.html',
            HAS_SOURCE:  true,
            SOURCELINK_SUFFIX: ''
        };
    </script>
      <script type="text/javascript" src="_static/jquery.js"></script>
      <script type="text/javascript" src="_static/underscore.js"></script>
      <script type="text/javascript" src="_static/doctools.js"></script>

  

  
  
    <script type="text/javascript" src="_static/js/theme.js"></script>
  

  
  
  <script type="text/javascript">
      jQuery(function () {
          SphinxRtdTheme.StickyNav.enable();
      });
  </script>
   

</body>
</html>